Variant report

Variant	rs3846046
Chromosome Location	chr3:112996316-112996317
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	EP300	chr3:112996309-112996593	GM12878	blood:	n/a	n/a
2	SPI1	chr3:112996256-112996596	GM12891	blood:	n/a	chr3:112996564-112996577
3	MEF2A	chr3:112996106-112996726	GM12878	blood:	n/a	n/a
4	CTCF	chr3:112996180-112996330	GM12864	blood:	n/a	n/a
5	MAZ	chr3:112996234-112996568	GM12878	blood:	n/a	n/a
6	WRNIP1	chr3:112996223-112996341	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:112995543..112998104-chr3:113010327..113013877,3	MCF-7	breast:
2	chr3:112994340..112996390-chr3:112999455..113002856,3	MCF-7	breast:

Variant related genes	Relation type
BOC	TF binding region
ENSG00000206530	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10511323	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11710894	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11715146	0.80[AMR][1000 genomes]
rs11717833	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11919134	0.81[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.91[AMR][1000 genomes]
rs11928342	0.84[AMR][1000 genomes]
rs12485329	0.86[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12492273	0.86[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.88[GIH][hapmap];0.81[JPT][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12494864	0.86[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.88[GIH][hapmap];0.81[JPT][hapmap];0.87[MEX][hapmap];0.86[TSI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12631733	0.95[CHB][hapmap];0.88[CHD][hapmap];0.82[JPT][hapmap];0.86[MEX][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12638030	0.95[CHB][hapmap];0.90[JPT][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs16860758	0.84[CEU][hapmap];0.88[CHB][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16860787	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16860792	0.87[AMR][1000 genomes]
rs16860899	0.80[JPT][hapmap]
rs2036282	0.86[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.88[GIH][hapmap];0.81[JPT][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2270781	0.91[JPT][hapmap]
rs34284771	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3814398	1.00[CHB][hapmap];0.84[CHD][hapmap];0.90[JPT][hapmap];0.86[MEX][hapmap];0.85[TSI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3856718	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3856719	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3856720	0.93[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41271357	0.93[AMR][1000 genomes]
rs4682131	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4682132	0.86[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4682478	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4682479	0.86[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.88[GIH][hapmap];0.81[JPT][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4682481	0.93[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4682483	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4682485	0.82[JPT][hapmap]
rs6809516	0.82[JPT][hapmap]
rs73235143	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73235147	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7641410	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs775222	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs775230	0.82[GIH][hapmap]
rs9820386	0.82[JPT][hapmap]
rs9857414	0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3431441	chr3:112453467-113213252	Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv829677	chr3:112857075-113038987	Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
3	nsv1013506	chr3:112890608-113680951	Weak transcription Bivalent/Poised TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
4	nsv877348	chr3:112914756-113012509	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3846046	CD96	cis	cerebellum	SCAN
rs3846046	BOC	cis	parietal	SCAN

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112973600-112997200	Weak transcription	Colonic Mucosa	Colon
2	chr3:112984800-112998400	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr3:112984800-113016400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr3:112988000-113003000	Strong transcription	Placenta Amnion	Placenta Amnion
5	chr3:112988400-112996800	Weak transcription	Placenta	Placenta
6	chr3:112989000-112997000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr3:112990400-113036000	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr3:112990600-113004000	Weak transcription	NHEK	skin
9	chr3:112991800-113006400	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr3:112993000-112997000	Weak transcription	Fetal Intestine Small	intestine
11	chr3:112993400-112996800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr3:112993400-112997400	Genic enhancers	Fetal Stomach	stomach
13	chr3:112993800-112996400	Enhancers	Brain Angular Gyrus	brain
14	chr3:112993800-112997000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr3:112993800-113036000	Weak transcription	Right Ventricle	heart
16	chr3:112994200-112997800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
17	chr3:112994400-112996400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
18	chr3:112994800-112997400	Weak transcription	Gastric	stomach
19	chr3:112995200-112996800	Weak transcription	Fetal Intestine Large	intestine
20	chr3:112995200-112997000	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr3:112995200-112997000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr3:112995200-112999400	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr3:112995200-113001200	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr3:112995200-113016000	Weak transcription	HUES6 Cell Line	embryonic stem cell
25	chr3:112995200-113022400	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr3:112995400-112996600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr3:112995400-112996800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr3:112995400-112996800	Weak transcription	Esophagus	oesophagus
29	chr3:112995400-112997000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr3:112995400-112997000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr3:112995400-112997000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr3:112995400-112997000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr3:112995400-112998200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr3:112995400-113006000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr3:112995400-113006200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr3:112995400-113024000	Weak transcription	Aorta	Aorta
37	chr3:112995400-113035800	Weak transcription	Lung	lung
38	chr3:112995600-112996800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
39	chr3:112995600-112996800	Enhancers	Primary B cells from cord blood	blood
40	chr3:112995600-112997000	Weak transcription	Fetal Brain Female	brain
41	chr3:112995600-112997200	Enhancers	Spleen	Spleen
42	chr3:112995600-112998200	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
43	chr3:112995600-113006400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr3:112995600-113008400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr3:112995800-112996400	Enhancers	Primary monocytes fromperipheralblood	blood
46	chr3:112995800-112996400	Enhancers	Brain Cingulate Gyrus	brain
47	chr3:112995800-112996400	Enhancers	Duodenum Mucosa	Duodenum
48	chr3:112995800-112996400	Enhancers	HSMM	muscle
49	chr3:112995800-112996600	Enhancers	Cortex derived primary cultured neurospheres	brain
50	chr3:112995800-112996800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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